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The negative equity problem for U.S. homeowners might be worse than previously thought, at least according to a new measure from Zillow(Z).

The online real estate data provider, in its first negative equity report, said 15.7 million, or 31.4%, of homeowners were underwater on their mortgages in the first quarter. That’s up from 31.1% three months earlier but down from 32.4% in the first quarter 2011.

Homeowners owed $1.2 trillion more than the value of their homes in the first quarter, according to Zillow.

“As home values slowly increase and these homeowners continue to pay down their principal, they will surface again,” Humphries said in a news release.

But Zillow’s measure is considerably higher — and subsequently more dire — than another report on negative equity among homeowners. A CoreLogic(CLGX) study from the fourth quarter 2011, the most recent available, tabulated roughly 11 million underwater homeowners, or 23% of all mortgaged properties.

Zillow said it analyzes available outstanding mortgage debt data, including lines of credit and first and second mortgages, provided by credit agency TransUnion. CoreLogic uses its own database of mortgages, which the company says accounts for roughly 85% of mortgages in the U.S.

Cynthia Nowak, a Zillow spokeswoman, said the company’s survey covers an estimated 50 million out of roughly 53 million mortgaged homes.

The differing numbers of underwater homeowners might have to do with the general problems of covering such a huge market, said Bill Emmons, an economist at the Federal Reserve Bank of St. Louis. There’s no absolute way to measure outstanding mortgage debt, he said, but the bigger difference likely comes from how each outlet measures home values.

“Even if you do come up with estimates for individual house values, it’s almost always assuming orderly market conditions,” Emmons said. “There is no answer or no solution to assigning values to something that hasn’t sold yet.”

The real issue, Emmons said, is that the different measures haven’t changed much. Zillow’s first-quarter reading fell just one percentage point from a year earlier, while CoreLogic’s fourth-quarter numbers came in at the same level as third-quarter 2009.

This negative equity and loads of debt present problems for the economy and skittish lenders, Emmons said. But for homeowners, the bigger harm is that negative equity raises the probability that other factors, like unemployment, could lead to default.

“It’s sort of like your immune system being compromised,” Emmons said. “You’re just more vulnerable to anything coming along.”

Even for a current borrower, negative equity makes it harder to move and to refinance their mortgage, said Fred Furlong, an economist at the Federal Reserve Bank of San Francisco.

But all households, even those from states that didn't see huge price drops, have cut back on nonmortgage debt on similar levels, Furlong said. It's as if "there has been a broader lesson" from the housing boom and bust, he said.

Zillow’s report is especially bleak for metropolitan areas in states hit hard by the housing crisis. Las Vegas led the country’s biggest cities with 71% of mortgaged homeowners underwater in the first quarter, followed by Phoenix at 55.5% and Atlanta at 55.2%.

Pittsburgh marked the low among big cities at 16.7%, trailed by New York at 21.3% and Boston at 22%.

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